I recently ran into a confusing issue with deletion mutagenesis. The approach I took to the deletion was to amply the entire plasmid, excluding the region to be deleted using 5' phosphorylated primers. PCR was followed by Dpn1 digest and ligation with T4 ligase. I transformed the PCR product into DH5a cells (cloning line) and prepared plasmid from individual colonies.

Sequencing shows that the deletion did work, however there is an additional base where the primers were ligated.

Specifically, the coding strand sequence should have read: ACC.CCT (ligation point is at the period)
and instead I got: ACCCCCT
Where the extra base causes a frameshift in the gene.

I should mention that all 3 colonies that had the deletion also had the extra cytosine.

Yes, I got the primers form Invitrogen, and the primer information matches what they should be. It may be possible that the primers are wrong, even though the company says they're OK, but I can't think how to check that.

I should also mention that another lab member has recently had the same problem, with an 'A' inserted where the blunt ends were ligated. At the time he thought that he had accidentally used Taq, which leaves an A-overhang. That can't be my problem though because my inserted base is a 'C'...

yeah i thot of that, A overhang could be explained but having extra 'C' is what intruding. Anyways i dnt have an explanation for this may be you redesign a new set of primers obviously the same sequence, and see how it goes.